Remove remaining deprecations, very old cmdstan version checks

Author: WardBrian

cmdstanpy/cmdstan_args.py

@@ -10,7 +10,7 @@
 import numpy as np
 from numpy.random import default_rng
 
-from cmdstanpy.utils import cmdstan_path, cmdstan_version_before, get_logger
+from cmdstanpy.utils import get_logger
 
 OptionalPath = str | os.PathLike | None
 
@@ -748,15 +748,6 @@ def validate(self) -> None:
                     'Argument "sig_figs" must be an integer between 1 and 18,'
                     ' found {}'.format(self.sig_figs)
                 )
-            # TODO: remove at some future release
-            if cmdstan_version_before(2, 25):
-                self.sig_figs = None
-                get_logger().warning(
-                    'Argument "sig_figs" invalid for CmdStan versions < 2.25, '
-                    'using version %s in directory %s',
-                    os.path.basename(cmdstan_path()),
-                    os.path.dirname(cmdstan_path()),
-                )
 
         if self.seed is None:
             rng = default_rng()

cmdstanpy/compilation.py

@@ -17,7 +17,6 @@
     EXTENSION,
     cmdstan_path,
     cmdstan_version,
-    cmdstan_version_before,
     stanc_path,
 )
 from cmdstanpy.utils.command import do_command
@@ -463,32 +462,13 @@ def format_stan_file(
         )
 
         if canonicalize:
-            if cmdstan_version_before(2, 29):
-                if isinstance(canonicalize, bool):
-                    cmd.append('--print-canonical')
-                else:
-                    raise ValueError(
-                        "Invalid arguments passed for current CmdStan"
-                        + " version({})\n".format(
-                            cmdstan_version() or "Unknown"
-                        )
-                        + "--canonicalize requires 2.29 or higher"
-                    )
+            if isinstance(canonicalize, str):
+                cmd.append('--canonicalize=' + canonicalize)
+            elif isinstance(canonicalize, Iterable):
+                cmd.append('--canonicalize=' + ','.join(canonicalize))
             else:
-                if isinstance(canonicalize, str):
-                    cmd.append('--canonicalize=' + canonicalize)
-                elif isinstance(canonicalize, Iterable):
-                    cmd.append('--canonicalize=' + ','.join(canonicalize))
-                else:
-                    cmd.append('--print-canonical')
-
-        # before 2.29, having both --print-canonical
-        # and --auto-format printed twice
-        if not (cmdstan_version_before(2, 29) and canonicalize):
-            cmd.append('--auto-format')
+                cmd.append('--print-canonical')
 
-        if not cmdstan_version_before(2, 29):
-            cmd.append(f'--max-line-length={max_line_length}')
         elif max_line_length != 78:
             raise ValueError(
                 "Invalid arguments passed for current CmdStan version"

cmdstanpy/install_cxx_toolchain.py

@@ -236,7 +236,7 @@ def get_toolchain_name() -> str:
     return ''
 
 
-# TODO(2.0): drop 3.5 support
+# TODO(2.0): consider something other than RTools
 def get_url(version: str) -> str:
     """Return URL for toolchain."""
     url = ''

cmdstanpy/model.py

@@ -13,7 +13,7 @@
 from concurrent.futures import ThreadPoolExecutor
 from io import StringIO
 from multiprocessing import cpu_count
-from typing import Any, Callable, Mapping, Sequence, TypeVar
+from typing import Any, Callable, Mapping, Sequence
 
 import numpy as np
 import pandas as pd
@@ -37,6 +37,7 @@
     CmdStanMLE,
     CmdStanPathfinder,
     CmdStanVB,
+    PrevFit,
     RunSet,
     from_csv,
 )
@@ -56,7 +57,6 @@
 from . import progress as progbar
 
 OptionalPath = str | os.PathLike | None
-Fit = TypeVar('Fit', CmdStanMCMC, CmdStanMLE, CmdStanVB)
 
 
 class CmdStanModel:
@@ -164,9 +164,7 @@ def __init__(
             )
 
             # try to detect models w/out parameters, needed for sampler
-            if (not cmdstan_version_before(2, 27)) and cmdstan_version_before(
-                2, 36
-            ):
+            if cmdstan_version_before(2, 36):
                 model_info = self.src_info()
                 if 'parameters' in model_info:
                     self._fixed_param |= len(model_info['parameters']) == 0
@@ -238,7 +236,7 @@ def src_info(self) -> dict[str, Any]:
         If stanc is older than 2.27 or if the stan
         file cannot be found, returns an empty dictionary.
         """
-        if self.stan_file is None or cmdstan_version_before(2, 27):
+        if self.stan_file is None:
             return {}
         return compilation.src_info(str(self.stan_file), self._stanc_options)
 
@@ -404,12 +402,6 @@ def optimize(
             jacobian=jacobian,
         )
 
-        if jacobian and cmdstan_version_before(2, 32, self.exe_info()):
-            raise ValueError(
-                "Jacobian adjustment for optimization is only supported "
-                "in CmdStan 2.32 and above."
-            )
-
         with (
             temp_single_json(data) as _data,
             temp_inits(inits, allow_multiple=False) as _inits,
@@ -734,34 +726,23 @@ def sample(
         if chains == 1:
             force_one_process_per_chain = True
 
-        if (
-            force_one_process_per_chain is None
-            and not cmdstan_version_before(2, 28, info_dict)
-            and stan_threads == 'true'
-        ):
+        if force_one_process_per_chain is None and stan_threads == 'true':
             one_process_per_chain = False
             num_threads = parallel_chains * num_threads
             parallel_procs = 1
         if force_one_process_per_chain is False:
-            if not cmdstan_version_before(2, 28, info_dict):
-                one_process_per_chain = False
-                num_threads = parallel_chains * num_threads
-                parallel_procs = 1
-                if stan_threads == 'false':
-                    get_logger().warning(
-                        'Stan program not compiled for threading, '
-                        'process will run chains sequentially. '
-                        'For multi-chain parallelization, recompile '
-                        'the model with argument '
-                        '"cpp_options={\'STAN_THREADS\':\'TRUE\'}.'
-                    )
-            else:
+            one_process_per_chain = False
+            num_threads = parallel_chains * num_threads
+            parallel_procs = 1
+            if stan_threads == 'false':
                 get_logger().warning(
-                    'Installed version of CmdStan cannot multi-process '
-                    'chains, will run %d processes. '
-                    'Run "install_cmdstan" to upgrade to latest version.',
-                    chains,
+                    'Stan program not compiled for threading, '
+                    'process will run chains sequentially. '
+                    'For multi-chain parallelization, recompile '
+                    'the model with argument '
+                    '"cpp_options={\'STAN_THREADS\':\'TRUE\'}.'
                 )
+
         os.environ['STAN_NUM_THREADS'] = str(num_threads)
 
         if chain_ids is None:
@@ -958,15 +939,15 @@ def sample(
     def generate_quantities(
         self,
         data: Mapping[str, Any] | str | os.PathLike | None = None,
-        previous_fit: Fit | list[str] | None = None,
+        previous_fit: PrevFit | list[str] | None = None,
         seed: int | None = None,
         gq_output_dir: OptionalPath = None,
         sig_figs: int | None = None,
         show_console: bool = False,
         refresh: int | None = None,
         time_fmt: str = "%Y%m%d%H%M%S",
         timeout: float | None = None,
-    ) -> CmdStanGQ[Fit]:
+    ) -> CmdStanGQ[PrevFit]:
         """
         Run CmdStan's generate_quantities method which runs the generated
         quantities block of a model given an existing sample.
@@ -1032,7 +1013,16 @@ def generate_quantities(
         :return: CmdStanGQ object
         """
 
-        if isinstance(previous_fit, (CmdStanMCMC, CmdStanMLE, CmdStanVB)):
+        if isinstance(
+            previous_fit,
+            (
+                CmdStanMCMC,
+                CmdStanMLE,
+                CmdStanVB,
+                CmdStanLaplace,
+                CmdStanPathfinder,
+            ),
+        ):
             fit_object = previous_fit
             fit_csv_files = previous_fit.runset.csv_files
         elif isinstance(previous_fit, list):
@@ -1042,7 +1032,7 @@ def generate_quantities(
                 )
             try:
                 fit_csv_files = previous_fit
-                fit_object: Fit = from_csv(fit_csv_files)  # type: ignore
+                fit_object: PrevFit = from_csv(fit_csv_files)  # type: ignore
             except ValueError as e:
                 raise ValueError(
                     'Invalid sample from Stan CSV files, error:\n\t{}\n\t'
@@ -1064,11 +1054,6 @@ def generate_quantities(
                     'to generate additional quantities of interest.'
                 )
         elif isinstance(fit_object, CmdStanMLE):
-            if cmdstan_version_before(2, 31):
-                raise RuntimeError(
-                    "Method generate_quantities was not "
-                    "available for non-HMC until CmdStan 2.31"
-                )
             chains = 1
             chain_ids = [1]
             if fit_object._save_iterations:
@@ -1077,11 +1062,6 @@ def generate_quantities(
                     'to generate additional quantities of interest.'
                 )
         else:  # isinstance(fit_object, CmdStanVB)
-            if cmdstan_version_before(2, 31):
-                raise RuntimeError(
-                    "Method generate_quantities was not "
-                    "available for non-HMC until CmdStan 2.31"
-                )
             chains = 1
             chain_ids = [1]
 
@@ -1492,19 +1472,6 @@ def pathfinder(
         """
 
         exe_info = self.exe_info()
-        if cmdstan_version_before(2, 33, exe_info):
-            raise ValueError(
-                "Method 'pathfinder' not available for CmdStan versions "
-                "before 2.33"
-            )
-
-        if (not psis_resample or not calculate_lp) and cmdstan_version_before(
-            2, 34, exe_info
-        ):
-            raise ValueError(
-                "Arguments 'psis_resample' and 'calculate_lp' are only "
-                "available for CmdStan versions 2.34 and later"
-            )
 
         if num_threads is not None:
             if (
@@ -1613,11 +1580,6 @@ def log_prob(
             unconstrained parameters of the model.
         """
 
-        if cmdstan_version_before(2, 31, self.exe_info()):
-            raise ValueError(
-                "Method 'log_prob' not available for CmdStan versions "
-                "before 2.31"
-            )
         with (
             temp_single_json(data) as _data,
             temp_single_json(params) as _params,
@@ -1729,11 +1691,7 @@ def laplace_sample(
 
         :return: A :class:`CmdStanLaplace` object.
         """
-        if cmdstan_version_before(2, 32, self.exe_info()):
-            raise ValueError(
-                "Method 'laplace_sample' not available for CmdStan versions "
-                "before 2.32"
-            )
+
         if opt_args is not None and mode is not None:
             raise ValueError(
                 "Cannot specify both 'opt_args' and 'mode' arguments"

cmdstanpy/stanfit/__init__.py

@@ -13,7 +13,7 @@
 )
 from cmdstanpy.utils import check_sampler_csv, get_logger, stancsv
 
-from .gq import CmdStanGQ
+from .gq import CmdStanGQ, PrevFit
 from .laplace import CmdStanLaplace
 from .mcmc import CmdStanMCMC
 from .metadata import InferenceMetadata
@@ -31,6 +31,7 @@
     "CmdStanGQ",
     "CmdStanLaplace",
     "CmdStanPathfinder",
+    "PrevFit",
 ]
 
 

cmdstanpy/stanfit/gq.py

@@ -35,16 +35,25 @@
     stancsv,
 )
 
+from .laplace import CmdStanLaplace
 from .mcmc import CmdStanMCMC
 from .metadata import InferenceMetadata
 from .mle import CmdStanMLE
+from .pathfinder import CmdStanPathfinder
 from .runset import RunSet
 from .vb import CmdStanVB
 
-Fit = TypeVar('Fit', CmdStanMCMC, CmdStanMLE, CmdStanVB)
+PrevFit = TypeVar(
+    'PrevFit',
+    CmdStanMCMC,
+    CmdStanMLE,
+    CmdStanVB,
+    CmdStanLaplace,
+    CmdStanPathfinder,
+)
 
 
-class CmdStanGQ(Generic[Fit]):
+class CmdStanGQ(Generic[PrevFit]):
     """
     Container for outputs from CmdStan generate_quantities run.
     Created by :meth:`CmdStanModel.generate_quantities`.
@@ -53,7 +62,7 @@ class CmdStanGQ(Generic[Fit]):
     def __init__(
         self,
         runset: RunSet,
-        previous_fit: Fit,
+        previous_fit: PrevFit,
     ) -> None:
         """Initialize object."""
         if not runset.method == Method.GENERATE_QUANTITIES:
@@ -63,7 +72,7 @@ def __init__(
             )
         self.runset = runset
 
-        self.previous_fit: Fit = previous_fit
+        self.previous_fit: PrevFit = previous_fit
 
         self._draws: np.ndarray = np.array(())
         self._metadata = self._validate_csv_files()
@@ -401,7 +410,12 @@ def draws_pd(
 
     @overload
     def draws_xr(
-        self: CmdStanGQ[CmdStanMLE] | CmdStanGQ[CmdStanVB],
+        self: (
+            CmdStanGQ[CmdStanMLE]
+            | CmdStanGQ[CmdStanVB]
+            | CmdStanGQ[CmdStanLaplace]
+            | CmdStanGQ[CmdStanPathfinder]
+        ),
         vars: str | list[str] | None = None,
         inc_warmup: bool = False,
         inc_sample: bool = False,
@@ -565,10 +579,7 @@ def stan_variable(self, var: str, **kwargs: bool) -> np.ndarray:
                 + ", ".join(model_var_names | gq_var_names)
             )
         if var not in gq_var_names:
-            # TODO(2.0) atleast1d may not be needed
-            return np.atleast_1d(  # type: ignore
-                self.previous_fit.stan_variable(var, **kwargs)
-            )
+            return self.previous_fit.stan_variable(var, **kwargs)
 
         # is gq variable
         self._assemble_generated_quantities()
@@ -718,11 +729,3 @@ def save_csvfiles(self, dir: str | None = None) -> None:
         cmdstanpy.from_csv
         """
         self.runset.save_csvfiles(dir)
-
-    # TODO(2.0): remove
-    @property
-    def mcmc_sample(self) -> CmdStanMCMC | CmdStanMLE | CmdStanVB:
-        get_logger().warning(
-            "Property `mcmc_sample` is deprecated, use `previous_fit` instead"
-        )
-        return self.previous_fit